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- PDB-1d1l: CRYSTAL STRUCTURE OF CRO-F58W MUTANT -

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Basic information

Entry
Database: PDB / ID: 1d1l
TitleCRYSTAL STRUCTURE OF CRO-F58W MUTANT
ComponentsLAMBDA CRO REPRESSOR
KeywordsVIRAL PROTEIN / HELIX-TURN-HELIX
Function / homology
Function and homology information


latency-replication decision / release from viral latency / negative regulation of transcription by competitive promoter binding / negative regulation of viral transcription / core promoter sequence-specific DNA binding / response to UV / protein homodimerization activity / DNA binding
Similarity search - Function
CRO Repressor / Regulatory protein cro superfamily / Cro / Regulatory protein cro / CRO Repressor / Lambda repressor-like, DNA-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Regulatory protein cro
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsRupert, P.B. / Mollah, A.K. / Mossing, M.C. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: The structural basis for enhanced stability and reduced DNA binding seen in engineered second-generation Cro monomers and dimers.
Authors: Rupert, P.B. / Mollah, A.K. / Mossing, M.C. / Matthews, B.W.
History
DepositionSep 17, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9792
Polymers6,8831
Non-polymers961
Water27015
1
A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,9584
Polymers13,7662
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
2
A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9168
Polymers27,5324
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area3420 Å2
ΔGint-93 kcal/mol
Surface area16660 Å2
MethodPISA
3
A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules

A: LAMBDA CRO REPRESSOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9168
Polymers27,5324
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area6160 Å2
ΔGint-59 kcal/mol
Surface area13930 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)59.860, 67.300, 91.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsThe biological assembly is a dimer constructed from chain A a symmetry partner generated by the two-fold.

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Components

#1: Protein LAMBDA CRO REPRESSOR


Mass: 6882.875 Da / Num. of mol.: 1 / Fragment: LAMBDA CRO REPRESSOR / Mutation: F58W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Genus: Lambda-like viruses / Production host: Escherichia coli (E. coli) / References: UniProt: P03040
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.2 M NH4SO4, 6% isopropanol, including a layer of Hampton's "Al's oil", pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.2 Mammonium sulfate1reservoir
26 %(w/v)isopropanol1reservoir
311 mg/mlprotein1drop
4Al's oil1drop

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.98
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jan 3, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 24029 / Num. obs: 5304 / % possible obs: 93 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rmerge(I) obs: 0.044
Reflection
*PLUS
Num. measured all: 24029

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→20 Å / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.258 530 -random
Rwork0.181 ---
all-5703 --
obs-5304 93 %-
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 5 15 504
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_bond_d0.014

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